FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
01-transhet-1_S1_merged_R1_001.fastq.gz 30,648,602 0 35-76 42
02-V1482Afs-4_S2_merged_R1_001.fastq.gz 36,211,072 0 51-76 43
03-WT-1_S3_merged_R1_001.fastq.gz 32,925,490 0 44-76 44
04-R122Pfs-1_S4_merged_R1_001.fastq.gz 33,969,739 0 48-76 43
05-transhet-4_S5_merged_R1_001.fastq.gz 34,736,323 0 47-76 44
06-transhet-2_S6_merged_R1_001.fastq.gz 35,118,762 0 46-76 43
07-WT-5_S7_merged_R1_001.fastq.gz 33,852,115 0 44-76 44
08-WT-3_S8_merged_R1_001.fastq.gz 31,560,153 0 47-76 43
09-transhet-3_S9_merged_R1_001.fastq.gz 32,846,763 0 48-76 44
10-R122Pfs-4_S10_merged_R1_001.fastq.gz 33,264,846 0 46-76 44
11-transhet-5_S11_merged_R1_001.fastq.gz 36,528,387 0 35-76 44
12-V1482Afs-1_S12_merged_R1_001.fastq.gz 37,751,699 0 47-76 44
13-R122Pfs-6_S13_merged_R1_001.fastq.gz 37,199,240 0 38-76 45
14-V1482Afs-2_S14_merged_R1_001.fastq.gz 35,788,848 0 35-76 45
15-WT-9_S15_merged_R1_001.fastq.gz 35,108,441 0 40-76 43
16-R122Pfs-3_S16_merged_R1_001.fastq.gz 34,667,603 0 43-76 43
17-V1482Afs-5_S17_merged_R1_001.fastq.gz 33,009,534 0 53-76 43
18-R122Pfs-2_S18_merged_R1_001.fastq.gz 33,966,690 0 52-76 44
19-transhet-6_S19_merged_R1_001.fastq.gz 33,911,443 0 40-76 44
20-WT-6_S20_merged_R1_001.fastq.gz 37,548,961 0 35-76 45
21-R122Pfs-5_S21_merged_R1_001.fastq.gz 35,014,462 0 43-76 45
22-V1482Afs-6_S22_merged_R1_001.fastq.gz 37,229,446 0 46-76 44
23-V1482Afs-3_S23_merged_R1_001.fastq.gz 34,874,523 0 40-76 44
24-WT-4_S24_merged_R1_001.fastq.gz 37,395,650 0 35-76 44

Read Totals

Library Sizes ranged between 30,648,602 and 37,751,699 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Hsapiens Genome

GC Content Distributions for all reads showing theoretical GC content from the Hsapiens Genome

Sequence Length Distribution

Sequence Duplication Levels

Adapter Content

Universal Adapter Content

Overrepresented Summary

Total overrepresented sequences for each library

Overrepresented Sequences

## Overrepresented_sequences missing from 01-transhet-1_S1_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 02-V1482Afs-4_S2_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 03-WT-1_S3_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 04-R122Pfs-1_S4_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 05-transhet-4_S5_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 06-transhet-2_S6_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 07-WT-5_S7_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 08-WT-3_S8_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 09-transhet-3_S9_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 10-R122Pfs-4_S10_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 11-transhet-5_S11_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 12-V1482Afs-1_S12_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 13-R122Pfs-6_S13_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 14-V1482Afs-2_S14_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 15-WT-9_S15_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 16-R122Pfs-3_S16_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 17-V1482Afs-5_S17_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 18-R122Pfs-2_S18_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 19-transhet-6_S19_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 20-WT-6_S20_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 21-R122Pfs-5_S21_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 22-V1482Afs-6_S22_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 23-V1482Afs-3_S23_merged_R1_001.fastq.gz
## Overrepresented_sequences missing from 24-WT-4_S24_merged_R1_001.fastq.gz
## No overrepresented sequences were detected by FastQC

Session Information

R version 3.6.0 (2019-04-26)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

locale: en_AU.UTF-8||en_AU.UTF-8||en_AU.UTF-8||C||en_AU.UTF-8||en_AU.UTF-8

attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: readr(v.1.3.1), stringr(v.1.4.0), magrittr(v.1.5), scales(v.1.1.0), pander(v.0.6.3), kableExtra(v.1.1.0), dplyr(v.0.8.3), ngsReports(v.1.0.1), tibble(v.2.1.3), ggplot2(v.3.2.1) and BiocGenerics(v.0.30.0)

loaded via a namespace (and not attached): bitops(v.1.0-6), matrixStats(v.0.55.0), lubridate(v.1.7.4), webshot(v.0.5.1), RColorBrewer(v.1.1-2), httr(v.1.4.1), GenomeInfoDb(v.1.20.0), tools(v.3.6.0), backports(v.1.1.5), R6(v.2.4.1), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.1.2), tidyselect(v.0.2.5), compiler(v.3.6.0), rvest(v.0.3.5), Biobase(v.2.44.0), xml2(v.1.2.2), DelayedArray(v.0.10.0), plotly(v.4.9.1), ggdendro(v.0.1-20), labeling(v.0.3), digest(v.0.6.22), Rsamtools(v.2.0.0), rmarkdown(v.1.17), XVector(v.0.24.0), pkgconfig(v.2.0.3), htmltools(v.0.4.0), fastmap(v.1.0.1), highr(v.0.8), htmlwidgets(v.1.5.1), rlang(v.0.4.1), rstudioapi(v.0.10), shiny(v.1.4.0), farver(v.2.0.1), zoo(v.1.8-7), hwriter(v.1.3.2), jsonlite(v.1.6), crosstalk(v.1.0.0), BiocParallel(v.1.18.0), RCurl(v.1.95-4.12), GenomeInfoDbData(v.1.2.1), Matrix(v.1.2-17), Rcpp(v.1.0.3), munsell(v.0.5.0), S4Vectors(v.0.22.0), lifecycle(v.0.1.0), stringi(v.1.4.3), yaml(v.2.2.0), MASS(v.7.3-51.4), SummarizedExperiment(v.1.14.0), zlibbioc(v.1.30.0), plyr(v.1.8.4), grid(v.3.6.0), promises(v.1.1.0), crayon(v.1.3.4), lattice(v.0.20-38), Biostrings(v.2.52.0), hms(v.0.5.2), zeallot(v.0.1.0), knitr(v.1.26), pillar(v.1.4.2), GenomicRanges(v.1.36.0), reshape2(v.1.4.3), stats4(v.3.6.0), glue(v.1.3.1), evaluate(v.0.14), ShortRead(v.1.42.0), latticeExtra(v.0.6-28), data.table(v.1.12.6), BiocManager(v.1.30.10), vctrs(v.0.2.0), httpuv(v.1.5.2), gtable(v.0.3.0), purrr(v.0.3.3), tidyr(v.1.0.0), assertthat(v.0.2.1), xfun(v.0.11), mime(v.0.7), xtable(v.1.8-4), later(v.1.0.0), viridisLite(v.0.3.0), truncnorm(v.1.0-8), GenomicAlignments(v.1.20.1), IRanges(v.2.18.1) and ellipsis(v.0.3.0)